Starting phenix.real_space_refine on Sat Feb 24 13:07:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvt_12612/02_2024/7nvt_12612.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvt_12612/02_2024/7nvt_12612.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvt_12612/02_2024/7nvt_12612.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvt_12612/02_2024/7nvt_12612.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvt_12612/02_2024/7nvt_12612.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvt_12612/02_2024/7nvt_12612.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.975 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 10 6.06 5 P 99 5.49 5 Mg 1 5.21 5 S 249 5.16 5 C 27540 2.51 5 N 7757 2.21 5 O 8458 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 657": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1076": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 814": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 935": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 96": "OE1" <-> "OE2" Residue "E GLU 97": "OE1" <-> "OE2" Residue "E PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 252": "OD1" <-> "OD2" Residue "Q PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 23": "NH1" <-> "NH2" Residue "W PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 29": "OE1" <-> "OE2" Residue "W ASP 35": "OD1" <-> "OD2" Residue "W GLU 46": "OE1" <-> "OE2" Residue "W GLU 50": "OE1" <-> "OE2" Residue "W ASP 83": "OD1" <-> "OD2" Residue "W PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 118": "OE1" <-> "OE2" Residue "W ASP 146": "OD1" <-> "OD2" Residue "W PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 192": "NH1" <-> "NH2" Residue "W ASP 196": "OD1" <-> "OD2" Residue "X PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 93": "OD1" <-> "OD2" Residue "X GLU 101": "OE1" <-> "OE2" Residue "X ASP 104": "OD1" <-> "OD2" Residue "X ASP 110": "OD1" <-> "OD2" Residue "X GLU 122": "OE1" <-> "OE2" Residue "X TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 147": "OD1" <-> "OD2" Residue "X ASP 213": "OD1" <-> "OD2" Residue "X GLU 214": "OE1" <-> "OE2" Residue "X GLU 235": "OE1" <-> "OE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 44114 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 11274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1423, 11274 Classifications: {'peptide': 1423} Link IDs: {'PCIS': 3, 'PTRANS': 67, 'TRANS': 1352} Chain breaks: 4 Chain: "B" Number of atoms: 9076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1136, 9076 Classifications: {'peptide': 1136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 53, 'TRANS': 1082} Chain breaks: 2 Chain: "C" Number of atoms: 2059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2059 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 15, 'TRANS': 241} Chain breaks: 1 Chain: "D" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1050 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 3, 'TRANS': 124} Chain: "E" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1721 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 636 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "G" Number of atoms: 1351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1351 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 928 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "J" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 507 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 373 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "M" Number of atoms: 1953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1953 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 13, 'TRANS': 238} Chain breaks: 1 Chain: "N" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1034 Classifications: {'DNA': 50} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 49} Chain: "O" Number of atoms: 1422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1422 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 9, 'TRANS': 169} Chain: "Q" Number of atoms: 1138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1138 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 7, 'TRANS': 130} Chain breaks: 1 Chain: "R" Number of atoms: 1788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1788 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain breaks: 1 Chain: "T" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1013 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain: "U" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 930 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 2, 'TRANS': 110} Chain breaks: 1 Chain: "V" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 806 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 1, 'TRANS': 97} Chain: "W" Number of atoms: 1535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1535 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 5, 'TRANS': 181} Chain: "X" Number of atoms: 1403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1403 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 5, 'TRANS': 165} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 464 SG CYS A 71 97.735 108.567 64.770 1.00 35.17 S ATOM 486 SG CYS A 74 97.759 106.056 61.908 1.00 33.79 S ATOM 533 SG CYS A 81 96.646 105.100 65.461 1.00 27.87 S ATOM 768 SG CYS A 111 138.954 83.261 70.361 1.00 42.25 S ATOM 796 SG CYS A 114 139.563 84.016 66.857 1.00 43.36 S ATOM 1109 SG CYS A 154 140.811 80.740 68.280 1.00 42.96 S ATOM 1132 SG CYS A 184 142.419 84.013 69.321 1.00 42.73 S ATOM 19919 SG CYS B1119 107.589 97.383 53.237 1.00 30.52 S ATOM 19941 SG CYS B1122 109.072 96.430 56.690 1.00 31.55 S ATOM 20056 SG CYS B1137 107.811 99.943 56.028 1.00 35.46 S ATOM 20077 SG CYS B1140 110.969 98.442 54.341 1.00 37.60 S ATOM 21044 SG CYS C 88 32.550 100.756 74.559 1.00 20.33 S ATOM 21057 SG CYS C 90 35.378 102.699 76.596 1.00 28.06 S ATOM 21092 SG CYS C 94 31.896 102.420 77.674 1.00 16.21 S ATOM 21114 SG CYS C 97 34.158 99.442 77.694 1.00 12.35 S ATOM 28400 SG CYS I 17 125.974 40.822 128.723 1.00 33.68 S ATOM 28424 SG CYS I 20 125.982 44.383 127.571 1.00 34.15 S ATOM 28585 SG CYS I 39 126.969 41.735 125.217 1.00 33.18 S ATOM 28610 SG CYS I 42 129.128 42.682 128.468 1.00 34.51 S ATOM 28962 SG CYS I 86 85.412 23.461 125.773 1.00 26.06 S ATOM 28986 SG CYS I 89 83.518 23.749 129.003 1.00 30.82 S ATOM 29190 SG CYS I 114 83.639 26.645 126.742 1.00 21.42 S ATOM 29225 SG CYS I 119 86.709 25.551 128.637 1.00 30.55 S ATOM 29336 SG CYS J 7 40.801 72.332 92.087 1.00 21.13 S ATOM 29360 SG CYS J 10 37.759 71.972 89.973 1.00 7.97 S ATOM 29624 SG CYS J 44 39.615 68.896 91.062 1.00 3.67 S ATOM 29630 SG CYS J 45 37.449 70.892 93.215 1.00 1.28 S ATOM 30750 SG CYS L 19 61.085 104.341 113.269 1.00 19.01 S ATOM 30769 SG CYS L 22 58.226 105.862 114.979 1.00 24.56 S ATOM 30886 SG CYS L 36 61.005 108.059 113.964 1.00 21.23 S ATOM 30912 SG CYS L 39 61.345 104.907 117.151 1.00 26.93 S ATOM 31094 SG CYS M 15 77.052 113.524 60.306 1.00 31.90 S ATOM 31241 SG CYS M 34 74.439 113.338 62.992 1.00 29.78 S ATOM 31263 SG CYS M 37 73.895 111.370 58.975 1.00 29.58 S ATOM 42163 SG CYS W 129 105.355 127.129 60.860 1.00 43.56 S ATOM 42183 SG CYS W 132 104.411 125.099 61.843 1.00 42.00 S ATOM 42355 SG CYS W 154 101.545 127.187 58.992 1.00 45.96 S Time building chain proxies: 23.45, per 1000 atoms: 0.53 Number of scatterers: 44114 At special positions: 0 Unit cell: (174.3, 172.2, 189, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 10 29.99 S 249 16.00 P 99 15.00 Mg 1 11.99 O 8458 8.00 N 7757 7.00 C 27540 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 20.01 Conformation dependent library (CDL) restraints added in 8.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" NE2 HIS A 84 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 74 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 81 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 71 " pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 111 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 114 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 184 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 154 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1140 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1122 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1119 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1137 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 94 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 97 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 17 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 42 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 39 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 89 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 119 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 114 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 86 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " pdb=" ZN M 401 " pdb="ZN ZN M 401 " - pdb=" ND1 HIS M 18 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 15 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 34 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 37 " pdb=" ZN W 501 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 129 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 132 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 154 " Number of angles added : 48 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9910 Finding SS restraints... Secondary structure from input PDB file: 194 helices and 0 sheets defined 36.6% alpha, 0.0% beta 44 base pairs and 81 stacking pairs defined. Time for finding SS restraints: 14.04 Creating SS restraints... Processing helix chain 'A' and resid 28 through 34 removed outlier: 3.642A pdb=" N LYS A 32 " --> pdb=" O PRO A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 109 removed outlier: 3.577A pdb=" N CYS A 109 " --> pdb=" O LYS A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 133 Processing helix chain 'A' and resid 137 through 149 removed outlier: 3.570A pdb=" N THR A 142 " --> pdb=" O LYS A 138 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU A 147 " --> pdb=" O HIS A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 227 removed outlier: 3.698A pdb=" N GLU A 223 " --> pdb=" O GLU A 219 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ILE A 224 " --> pdb=" O ARG A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 235 Processing helix chain 'A' and resid 245 through 248 No H-bonds generated for 'chain 'A' and resid 245 through 248' Processing helix chain 'A' and resid 275 through 296 Processing helix chain 'A' and resid 300 through 318 Processing helix chain 'A' and resid 339 through 343 Processing helix chain 'A' and resid 349 through 352 No H-bonds generated for 'chain 'A' and resid 349 through 352' Processing helix chain 'A' and resid 382 through 387 Processing helix chain 'A' and resid 399 through 408 Processing helix chain 'A' and resid 435 through 438 Processing helix chain 'A' and resid 466 through 468 No H-bonds generated for 'chain 'A' and resid 466 through 468' Processing helix chain 'A' and resid 486 through 492 removed outlier: 3.514A pdb=" N THR A 489 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR A 490 " --> pdb=" O SER A 487 " (cutoff:3.500A) Proline residue: A 491 - end of helix No H-bonds generated for 'chain 'A' and resid 486 through 492' Processing helix chain 'A' and resid 509 through 518 Processing helix chain 'A' and resid 522 through 524 No H-bonds generated for 'chain 'A' and resid 522 through 524' Processing helix chain 'A' and resid 539 through 548 Processing helix chain 'A' and resid 557 through 566 removed outlier: 3.621A pdb=" N MET A 565 " --> pdb=" O MET A 561 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N PHE A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 595 removed outlier: 3.592A pdb=" N LEU A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 645 No H-bonds generated for 'chain 'A' and resid 642 through 645' Processing helix chain 'A' and resid 652 through 660 Processing helix chain 'A' and resid 662 through 683 removed outlier: 3.678A pdb=" N LEU A 681 " --> pdb=" O ASN A 677 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 691 No H-bonds generated for 'chain 'A' and resid 689 through 691' Processing helix chain 'A' and resid 696 through 721 Processing helix chain 'A' and resid 733 through 759 Processing helix chain 'A' and resid 765 through 772 Processing helix chain 'A' and resid 778 through 785 Processing helix chain 'A' and resid 817 through 820 No H-bonds generated for 'chain 'A' and resid 817 through 820' Processing helix chain 'A' and resid 833 through 856 removed outlier: 3.571A pdb=" N GLU A 845 " --> pdb=" O MET A 841 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLY A 846 " --> pdb=" O GLY A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 868 removed outlier: 3.697A pdb=" N LYS A 866 " --> pdb=" O ARG A 862 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N SER A 867 " --> pdb=" O ARG A 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 893 No H-bonds generated for 'chain 'A' and resid 891 through 893' Processing helix chain 'A' and resid 907 through 910 No H-bonds generated for 'chain 'A' and resid 907 through 910' Processing helix chain 'A' and resid 913 through 920 Processing helix chain 'A' and resid 927 through 933 Processing helix chain 'A' and resid 936 through 944 Processing helix chain 'A' and resid 946 through 969 Processing helix chain 'A' and resid 983 through 993 Processing helix chain 'A' and resid 1006 through 1019 removed outlier: 3.504A pdb=" N LYS A1019 " --> pdb=" O GLU A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1037 Processing helix chain 'A' and resid 1039 through 1048 Processing helix chain 'A' and resid 1051 through 1056 Processing helix chain 'A' and resid 1062 through 1077 Processing helix chain 'A' and resid 1087 through 1101 Proline residue: A1098 - end of helix removed outlier: 4.032A pdb=" N GLN A1101 " --> pdb=" O GLU A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1128 Processing helix chain 'A' and resid 1146 through 1149 No H-bonds generated for 'chain 'A' and resid 1146 through 1149' Processing helix chain 'A' and resid 1151 through 1161 Processing helix chain 'A' and resid 1166 through 1169 No H-bonds generated for 'chain 'A' and resid 1166 through 1169' Processing helix chain 'A' and resid 1187 through 1197 removed outlier: 4.087A pdb=" N GLU A1191 " --> pdb=" O ALA A1187 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N TRP A1192 " --> pdb=" O GLU A1188 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N VAL A1195 " --> pdb=" O GLU A1191 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR A1196 " --> pdb=" O TRP A1192 " (cutoff:3.500A) Processing helix chain 'A' and resid 1218 through 1223 Processing helix chain 'A' and resid 1228 through 1239 removed outlier: 3.691A pdb=" N ALA A1232 " --> pdb=" O MET A1228 " (cutoff:3.500A) Processing helix chain 'A' and resid 1263 through 1266 No H-bonds generated for 'chain 'A' and resid 1263 through 1266' Processing helix chain 'A' and resid 1283 through 1294 Processing helix chain 'A' and resid 1343 through 1348 Processing helix chain 'A' and resid 1362 through 1368 Processing helix chain 'A' and resid 1371 through 1389 removed outlier: 4.809A pdb=" N ASP A1389 " --> pdb=" O VAL A1385 " (cutoff:3.500A) Processing helix chain 'A' and resid 1395 through 1406 Processing helix chain 'A' and resid 1416 through 1421 removed outlier: 3.943A pdb=" N ARG A1421 " --> pdb=" O HIS A1417 " (cutoff:3.500A) Processing helix chain 'A' and resid 1426 through 1432 removed outlier: 3.501A pdb=" N PHE A1432 " --> pdb=" O MET A1428 " (cutoff:3.500A) Processing helix chain 'A' and resid 1435 through 1445 removed outlier: 3.621A pdb=" N LEU A1439 " --> pdb=" O THR A1435 " (cutoff:3.500A) Processing helix chain 'A' and resid 1454 through 1459 Processing helix chain 'A' and resid 1467 through 1469 No H-bonds generated for 'chain 'A' and resid 1467 through 1469' Processing helix chain 'A' and resid 1477 through 1481 Processing helix chain 'B' and resid 19 through 37 removed outlier: 4.428A pdb=" N GLN B 23 " --> pdb=" O PRO B 19 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N GLU B 24 " --> pdb=" O ASP B 20 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TRP B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 52 Processing helix chain 'B' and resid 54 through 61 Processing helix chain 'B' and resid 110 through 116 Processing helix chain 'B' and resid 168 through 174 Processing helix chain 'B' and resid 249 through 252 No H-bonds generated for 'chain 'B' and resid 249 through 252' Processing helix chain 'B' and resid 269 through 276 Processing helix chain 'B' and resid 281 through 288 removed outlier: 3.617A pdb=" N HIS B 287 " --> pdb=" O ASP B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 307 removed outlier: 3.674A pdb=" N VAL B 301 " --> pdb=" O MET B 297 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS B 302 " --> pdb=" O MET B 298 " (cutoff:3.500A) Proline residue: B 303 - end of helix Processing helix chain 'B' and resid 314 through 324 removed outlier: 3.517A pdb=" N ARG B 324 " --> pdb=" O PHE B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 345 Processing helix chain 'B' and resid 358 through 377 Processing helix chain 'B' and resid 388 through 390 No H-bonds generated for 'chain 'B' and resid 388 through 390' Processing helix chain 'B' and resid 396 through 425 removed outlier: 3.504A pdb=" N GLY B 406 " --> pdb=" O PHE B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 434 No H-bonds generated for 'chain 'B' and resid 431 through 434' Processing helix chain 'B' and resid 437 through 450 removed outlier: 3.529A pdb=" N SER B 441 " --> pdb=" O ARG B 438 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASP B 442 " --> pdb=" O ILE B 439 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY B 443 " --> pdb=" O ILE B 440 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU B 444 " --> pdb=" O SER B 441 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS B 445 " --> pdb=" O ASP B 442 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TYR B 446 " --> pdb=" O GLY B 443 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER B 447 " --> pdb=" O LEU B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 458 No H-bonds generated for 'chain 'B' and resid 456 through 458' Processing helix chain 'B' and resid 475 through 483 Processing helix chain 'B' and resid 490 through 495 removed outlier: 3.749A pdb=" N LYS B 494 " --> pdb=" O GLY B 490 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU B 495 " --> pdb=" O ARG B 491 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 490 through 495' Processing helix chain 'B' and resid 503 through 505 No H-bonds generated for 'chain 'B' and resid 503 through 505' Processing helix chain 'B' and resid 539 through 547 Processing helix chain 'B' and resid 558 through 561 Processing helix chain 'B' and resid 580 through 592 Processing helix chain 'B' and resid 637 through 644 Processing helix chain 'B' and resid 653 through 658 Processing helix chain 'B' and resid 667 through 672 removed outlier: 3.611A pdb=" N GLU B 671 " --> pdb=" O THR B 667 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N THR B 672 " --> pdb=" O LEU B 668 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 667 through 672' Processing helix chain 'B' and resid 679 through 682 No H-bonds generated for 'chain 'B' and resid 679 through 682' Processing helix chain 'B' and resid 700 through 703 Processing helix chain 'B' and resid 714 through 716 No H-bonds generated for 'chain 'B' and resid 714 through 716' Processing helix chain 'B' and resid 719 through 731 removed outlier: 3.863A pdb=" N LYS B 730 " --> pdb=" O SER B 726 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN B 731 " --> pdb=" O ALA B 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 765 Processing helix chain 'B' and resid 798 through 803 Processing helix chain 'B' and resid 951 through 953 No H-bonds generated for 'chain 'B' and resid 951 through 953' Processing helix chain 'B' and resid 969 through 975 Proline residue: B 973 - end of helix Processing helix chain 'B' and resid 978 through 993 Processing helix chain 'B' and resid 1008 through 1018 removed outlier: 3.634A pdb=" N ASP B1017 " --> pdb=" O ASN B1013 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N TYR B1018 " --> pdb=" O LEU B1014 " (cutoff:3.500A) Processing helix chain 'B' and resid 1088 through 1097 Processing helix chain 'B' and resid 1100 through 1107 Processing helix chain 'B' and resid 1109 through 1112 No H-bonds generated for 'chain 'B' and resid 1109 through 1112' Processing helix chain 'B' and resid 1153 through 1165 removed outlier: 3.623A pdb=" N MET B1165 " --> pdb=" O GLU B1161 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 40 Processing helix chain 'C' and resid 61 through 69 Processing helix chain 'C' and resid 78 through 81 No H-bonds generated for 'chain 'C' and resid 78 through 81' Processing helix chain 'C' and resid 117 through 119 No H-bonds generated for 'chain 'C' and resid 117 through 119' Processing helix chain 'C' and resid 174 through 176 No H-bonds generated for 'chain 'C' and resid 174 through 176' Processing helix chain 'C' and resid 200 through 202 No H-bonds generated for 'chain 'C' and resid 200 through 202' Processing helix chain 'C' and resid 241 through 270 removed outlier: 3.710A pdb=" N VAL C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 26 No H-bonds generated for 'chain 'D' and resid 24 through 26' Processing helix chain 'D' and resid 34 through 49 Processing helix chain 'D' and resid 59 through 71 Processing helix chain 'D' and resid 77 through 89 Processing helix chain 'D' and resid 94 through 103 Processing helix chain 'D' and resid 108 through 114 Processing helix chain 'D' and resid 116 through 118 No H-bonds generated for 'chain 'D' and resid 116 through 118' Processing helix chain 'D' and resid 124 through 137 Processing helix chain 'E' and resid 3 through 24 removed outlier: 3.965A pdb=" N THR E 7 " --> pdb=" O ASP E 3 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N TYR E 8 " --> pdb=" O GLU E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 33 No H-bonds generated for 'chain 'E' and resid 30 through 33' Processing helix chain 'E' and resid 37 through 44 removed outlier: 3.567A pdb=" N PHE E 44 " --> pdb=" O PHE E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 97 removed outlier: 3.986A pdb=" N GLU E 97 " --> pdb=" O ARG E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 120 Processing helix chain 'E' and resid 132 through 136 Processing helix chain 'E' and resid 139 through 141 No H-bonds generated for 'chain 'E' and resid 139 through 141' Processing helix chain 'E' and resid 153 through 163 Processing helix chain 'E' and resid 167 through 169 No H-bonds generated for 'chain 'E' and resid 167 through 169' Processing helix chain 'E' and resid 178 through 183 Processing helix chain 'F' and resid 59 through 74 Processing helix chain 'F' and resid 89 through 99 Processing helix chain 'F' and resid 120 through 122 No H-bonds generated for 'chain 'F' and resid 120 through 122' Processing helix chain 'G' and resid 15 through 17 No H-bonds generated for 'chain 'G' and resid 15 through 17' Processing helix chain 'G' and resid 22 through 34 Processing helix chain 'H' and resid 84 through 87 Processing helix chain 'I' and resid 64 through 67 No H-bonds generated for 'chain 'I' and resid 64 through 67' Processing helix chain 'I' and resid 70 through 74 Processing helix chain 'J' and resid 18 through 26 Processing helix chain 'J' and resid 31 through 37 Processing helix chain 'J' and resid 43 through 50 removed outlier: 3.703A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 61 removed outlier: 3.901A pdb=" N ASN J 61 " --> pdb=" O GLU J 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 9 removed outlier: 3.643A pdb=" N SER K 9 " --> pdb=" O ALA K 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 6 through 9' Processing helix chain 'K' and resid 40 through 52 removed outlier: 3.598A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 114 Processing helix chain 'M' and resid 48 through 51 No H-bonds generated for 'chain 'M' and resid 48 through 51' Processing helix chain 'M' and resid 109 through 128 removed outlier: 3.504A pdb=" N ARG M 127 " --> pdb=" O THR M 123 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE M 128 " --> pdb=" O MET M 124 " (cutoff:3.500A) Processing helix chain 'M' and resid 132 through 148 Processing helix chain 'M' and resid 156 through 170 Processing helix chain 'M' and resid 177 through 182 Processing helix chain 'M' and resid 188 through 202 Processing helix chain 'M' and resid 211 through 213 No H-bonds generated for 'chain 'M' and resid 211 through 213' Processing helix chain 'M' and resid 215 through 221 Processing helix chain 'M' and resid 226 through 242 Processing helix chain 'M' and resid 250 through 264 Processing helix chain 'M' and resid 271 through 278 Processing helix chain 'M' and resid 282 through 299 Proline residue: M 294 - end of helix Proline residue: M 297 - end of helix Processing helix chain 'M' and resid 310 through 312 No H-bonds generated for 'chain 'M' and resid 310 through 312' Processing helix chain 'O' and resid 180 through 186 Processing helix chain 'O' and resid 227 through 243 Processing helix chain 'O' and resid 270 through 276 Processing helix chain 'O' and resid 318 through 335 Proline residue: O 330 - end of helix Processing helix chain 'Q' and resid 6 through 9 No H-bonds generated for 'chain 'Q' and resid 6 through 9' Processing helix chain 'Q' and resid 33 through 35 No H-bonds generated for 'chain 'Q' and resid 33 through 35' Processing helix chain 'Q' and resid 157 through 166 removed outlier: 3.905A pdb=" N GLU Q 162 " --> pdb=" O GLU Q 158 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU Q 165 " --> pdb=" O GLU Q 161 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ARG Q 166 " --> pdb=" O GLU Q 162 " (cutoff:3.500A) Processing helix chain 'Q' and resid 173 through 179 removed outlier: 4.220A pdb=" N MET Q 177 " --> pdb=" O HIS Q 173 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN Q 178 " --> pdb=" O PHE Q 174 " (cutoff:3.500A) Processing helix chain 'R' and resid 10 through 14 Processing helix chain 'R' and resid 25 through 34 removed outlier: 4.063A pdb=" N ALA R 34 " --> pdb=" O GLN R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 63 No H-bonds generated for 'chain 'R' and resid 60 through 63' Processing helix chain 'R' and resid 122 through 138 removed outlier: 4.146A pdb=" N ARG R 126 " --> pdb=" O GLU R 122 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU R 127 " --> pdb=" O ASN R 123 " (cutoff:3.500A) Proline residue: R 138 - end of helix Processing helix chain 'R' and resid 160 through 172 Processing helix chain 'R' and resid 180 through 192 removed outlier: 4.048A pdb=" N GLU R 192 " --> pdb=" O PHE R 188 " (cutoff:3.500A) Processing helix chain 'R' and resid 199 through 206 Processing helix chain 'R' and resid 210 through 220 removed outlier: 3.568A pdb=" N ILE R 220 " --> pdb=" O ILE R 216 " (cutoff:3.500A) Processing helix chain 'U' and resid 10 through 32 removed outlier: 4.400A pdb=" N ASP U 27 " --> pdb=" O ASN U 23 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ILE U 28 " --> pdb=" O ASP U 24 " (cutoff:3.500A) Processing helix chain 'U' and resid 36 through 50 removed outlier: 3.562A pdb=" N LYS U 43 " --> pdb=" O MET U 40 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU U 45 " --> pdb=" O LEU U 42 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS U 49 " --> pdb=" O TRP U 46 " (cutoff:3.500A) Processing helix chain 'U' and resid 326 through 329 No H-bonds generated for 'chain 'U' and resid 326 through 329' Processing helix chain 'V' and resid 10 through 24 Processing helix chain 'V' and resid 30 through 51 Processing helix chain 'W' and resid 12 through 25 removed outlier: 3.519A pdb=" N LYS W 19 " --> pdb=" O LYS W 15 " (cutoff:3.500A) Processing helix chain 'W' and resid 28 through 39 Processing helix chain 'W' and resid 45 through 52 Processing helix chain 'W' and resid 56 through 68 Processing helix chain 'W' and resid 96 through 123 removed outlier: 3.722A pdb=" N ASN W 101 " --> pdb=" O ARG W 97 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N MET W 110 " --> pdb=" O LYS W 106 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE W 114 " --> pdb=" O MET W 110 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N GLU W 115 " --> pdb=" O ARG W 111 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR W 116 " --> pdb=" O ARG W 112 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP W 120 " --> pdb=" O THR W 116 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER W 121 " --> pdb=" O ASP W 117 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR W 122 " --> pdb=" O GLU W 118 " (cutoff:3.500A) Processing helix chain 'W' and resid 138 through 144 removed outlier: 3.658A pdb=" N ASN W 142 " --> pdb=" O ASP W 138 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN W 143 " --> pdb=" O LEU W 139 " (cutoff:3.500A) Processing helix chain 'W' and resid 165 through 195 Proline residue: W 169 - end of helix removed outlier: 3.602A pdb=" N ASP W 172 " --> pdb=" O MET W 168 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG W 174 " --> pdb=" O LYS W 170 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR W 175 " --> pdb=" O LYS W 171 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA W 178 " --> pdb=" O ARG W 174 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU W 182 " --> pdb=" O ALA W 178 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLN W 183 " --> pdb=" O ARG W 179 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE W 184 " --> pdb=" O PHE W 180 " (cutoff:3.500A) Proline residue: W 186 - end of helix removed outlier: 3.771A pdb=" N ALA W 189 " --> pdb=" O GLU W 185 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG W 192 " --> pdb=" O TYR W 188 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLU W 193 " --> pdb=" O ALA W 189 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N THR W 194 " --> pdb=" O LEU W 190 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU W 195 " --> pdb=" O LEU W 191 " (cutoff:3.500A) Processing helix chain 'X' and resid 76 through 91 removed outlier: 3.548A pdb=" N LYS X 80 " --> pdb=" O GLY X 76 " (cutoff:3.500A) Processing helix chain 'X' and resid 99 through 105 removed outlier: 3.823A pdb=" N GLU X 105 " --> pdb=" O GLU X 101 " (cutoff:3.500A) Processing helix chain 'X' and resid 113 through 121 Processing helix chain 'X' and resid 123 through 126 No H-bonds generated for 'chain 'X' and resid 123 through 126' Processing helix chain 'X' and resid 148 through 161 Processing helix chain 'X' and resid 168 through 174 Processing helix chain 'X' and resid 178 through 188 removed outlier: 5.956A pdb=" N ASP X 187 " --> pdb=" O LYS X 183 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N GLN X 188 " --> pdb=" O ALA X 184 " (cutoff:3.500A) Processing helix chain 'X' and resid 214 through 222 Processing helix chain 'X' and resid 230 through 240 removed outlier: 4.079A pdb=" N LEU X 237 " --> pdb=" O ILE X 233 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS X 238 " --> pdb=" O GLU X 234 " (cutoff:3.500A) 1046 hydrogen bonds defined for protein. 3075 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 117 hydrogen bonds 234 hydrogen bond angles 0 basepair planarities 44 basepair parallelities 81 stacking parallelities Total time for adding SS restraints: 14.94 Time building geometry restraints manager: 21.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 14394 1.34 - 1.46: 9880 1.46 - 1.58: 20266 1.58 - 1.71: 197 1.71 - 1.83: 392 Bond restraints: 45129 Sorted by residual: bond pdb=" N MET V 1 " pdb=" CA MET V 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.02e+00 bond pdb=" N MET G 1 " pdb=" CA MET G 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.92e+00 bond pdb=" N MET K 1 " pdb=" CA MET K 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.75e+00 bond pdb=" N MET J 1 " pdb=" CA MET J 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.75e+00 bond pdb=" CZ ARG A 483 " pdb=" NH2 ARG A 483 " ideal model delta sigma weight residual 1.330 1.313 0.017 1.30e-02 5.92e+03 1.70e+00 ... (remaining 45124 not shown) Histogram of bond angle deviations from ideal: 99.55 - 106.44: 1736 106.44 - 113.33: 24682 113.33 - 120.22: 15875 120.22 - 127.11: 18425 127.11 - 134.00: 634 Bond angle restraints: 61352 Sorted by residual: angle pdb=" CA VAL K 27 " pdb=" C VAL K 27 " pdb=" N PRO K 28 " ideal model delta sigma weight residual 116.57 119.42 -2.85 9.80e-01 1.04e+00 8.46e+00 angle pdb=" N ILE A1486 " pdb=" CA ILE A1486 " pdb=" C ILE A1486 " ideal model delta sigma weight residual 112.35 109.33 3.02 1.20e+00 6.94e-01 6.35e+00 angle pdb=" N LYS O 297 " pdb=" CA LYS O 297 " pdb=" C LYS O 297 " ideal model delta sigma weight residual 112.75 109.35 3.40 1.36e+00 5.41e-01 6.26e+00 angle pdb=" N ASP B 681 " pdb=" CA ASP B 681 " pdb=" C ASP B 681 " ideal model delta sigma weight residual 114.56 111.48 3.08 1.27e+00 6.20e-01 5.90e+00 angle pdb=" N GLN A 539 " pdb=" CA GLN A 539 " pdb=" C GLN A 539 " ideal model delta sigma weight residual 110.80 115.97 -5.17 2.13e+00 2.20e-01 5.90e+00 ... (remaining 61347 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.16: 26289 31.16 - 62.31: 1036 62.31 - 93.47: 74 93.47 - 124.63: 0 124.63 - 155.79: 2 Dihedral angle restraints: 27401 sinusoidal: 12103 harmonic: 15298 Sorted by residual: dihedral pdb=" CA VAL A 538 " pdb=" C VAL A 538 " pdb=" N GLN A 539 " pdb=" CA GLN A 539 " ideal model delta harmonic sigma weight residual -180.00 -153.05 -26.95 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" CA LYS O 297 " pdb=" C LYS O 297 " pdb=" N PRO O 298 " pdb=" CA PRO O 298 " ideal model delta harmonic sigma weight residual 180.00 154.79 25.21 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA ILE C 39 " pdb=" C ILE C 39 " pdb=" N ALA C 40 " pdb=" CA ALA C 40 " ideal model delta harmonic sigma weight residual 180.00 -160.19 -19.81 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 27398 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 4788 0.033 - 0.066: 1309 0.066 - 0.099: 436 0.099 - 0.132: 303 0.132 - 0.165: 8 Chirality restraints: 6844 Sorted by residual: chirality pdb=" CA PRO A 478 " pdb=" N PRO A 478 " pdb=" C PRO A 478 " pdb=" CB PRO A 478 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.16 2.00e-01 2.50e+01 6.78e-01 chirality pdb=" CA ILE B 152 " pdb=" N ILE B 152 " pdb=" C ILE B 152 " pdb=" CB ILE B 152 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.26e-01 chirality pdb=" CA ILE B 965 " pdb=" N ILE B 965 " pdb=" C ILE B 965 " pdb=" CB ILE B 965 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.96e-01 ... (remaining 6841 not shown) Planarity restraints: 7605 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS M 18 " -0.020 2.00e-02 2.50e+03 2.23e-02 7.44e+00 pdb=" CG HIS M 18 " 0.042 2.00e-02 2.50e+03 pdb=" ND1 HIS M 18 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 HIS M 18 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS M 18 " 0.011 2.00e-02 2.50e+03 pdb=" NE2 HIS M 18 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS O 297 " 0.044 5.00e-02 4.00e+02 6.72e-02 7.22e+00 pdb=" N PRO O 298 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO O 298 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO O 298 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 477 " -0.026 5.00e-02 4.00e+02 3.94e-02 2.49e+00 pdb=" N PRO A 478 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 478 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 478 " -0.022 5.00e-02 4.00e+02 ... (remaining 7602 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 438 2.56 - 3.15: 36808 3.15 - 3.73: 72468 3.73 - 4.32: 104371 4.32 - 4.90: 167762 Nonbonded interactions: 381847 Sorted by model distance: nonbonded pdb=" O ALA R 190 " pdb=" OH TYR R 197 " model vdw 1.979 2.440 nonbonded pdb=" O MET A 535 " pdb=" OH TYR A 669 " model vdw 2.008 2.440 nonbonded pdb=" OH TYR B 814 " pdb=" OE1 GLU B 900 " model vdw 2.015 2.440 nonbonded pdb=" O PRO A 911 " pdb=" NH2 ARG A 963 " model vdw 2.059 2.520 nonbonded pdb=" O ALA E 114 " pdb=" OG SER E 117 " model vdw 2.079 2.440 ... (remaining 381842 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 20.700 Check model and map are aligned: 0.700 Set scattering table: 0.430 Process input model: 129.610 Find NCS groups from input model: 1.490 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:11.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 168.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 45129 Z= 0.206 Angle : 0.466 7.224 61352 Z= 0.270 Chirality : 0.040 0.165 6844 Planarity : 0.003 0.067 7605 Dihedral : 15.596 155.785 17491 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.12), residues: 5187 helix: 1.98 (0.12), residues: 1895 sheet: 0.76 (0.18), residues: 840 loop : 0.24 (0.13), residues: 2452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 453 HIS 0.025 0.001 HIS M 18 PHE 0.022 0.001 PHE B 918 TYR 0.020 0.001 TYR K 81 ARG 0.023 0.000 ARG E 52 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1000 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1000 time to evaluate : 5.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 841 MET cc_start: 0.8984 (mtp) cc_final: 0.8758 (mtp) REVERT: A 861 GLN cc_start: 0.8357 (tt0) cc_final: 0.8096 (mt0) REVERT: A 960 ARG cc_start: 0.7428 (ttm-80) cc_final: 0.7079 (ttm-80) REVERT: A 1484 MET cc_start: 0.5014 (pmm) cc_final: 0.4812 (pmm) REVERT: B 840 MET cc_start: 0.3979 (mtp) cc_final: 0.3299 (pmm) REVERT: B 1125 MET cc_start: 0.8047 (mtm) cc_final: 0.7806 (mtm) REVERT: E 125 TYR cc_start: 0.5899 (m-80) cc_final: 0.5662 (m-80) REVERT: H 33 GLU cc_start: 0.6817 (pm20) cc_final: 0.6420 (pm20) REVERT: I 54 TYR cc_start: 0.7150 (t80) cc_final: 0.6858 (t80) REVERT: K 22 ASN cc_start: 0.8095 (m-40) cc_final: 0.7830 (m-40) REVERT: K 23 LYS cc_start: 0.8108 (ttmt) cc_final: 0.7874 (tptt) REVERT: Q 31 PHE cc_start: 0.7196 (m-80) cc_final: 0.6738 (m-80) REVERT: U 51 MET cc_start: 0.2209 (mmp) cc_final: 0.1575 (mpm) REVERT: W 110 MET cc_start: 0.1485 (mmt) cc_final: 0.1063 (mmt) outliers start: 0 outliers final: 2 residues processed: 1000 average time/residue: 1.7410 time to fit residues: 2106.1419 Evaluate side-chains 643 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 641 time to evaluate : 5.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain E residue 57 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 524 random chunks: chunk 442 optimal weight: 30.0000 chunk 397 optimal weight: 0.4980 chunk 220 optimal weight: 1.9990 chunk 135 optimal weight: 8.9990 chunk 267 optimal weight: 0.0470 chunk 212 optimal weight: 1.9990 chunk 410 optimal weight: 10.0000 chunk 158 optimal weight: 0.9980 chunk 249 optimal weight: 2.9990 chunk 305 optimal weight: 3.9990 chunk 475 optimal weight: 0.3980 overall best weight: 0.7880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 HIS A 410 ASN A 723 ASN ** A1194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1220 HIS ** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 500 GLN B 503 ASN B 941 GLN ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 ASN C 217 GLN C 260 GLN E 116 GLN G 28 GLN I 22 ASN M 221 ASN M 263 GLN ** O 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 129 GLN R 223 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 45129 Z= 0.255 Angle : 0.574 11.309 61352 Z= 0.295 Chirality : 0.043 0.209 6844 Planarity : 0.004 0.065 7605 Dihedral : 12.923 152.225 6815 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.60 % Favored : 97.38 % Rotamer: Outliers : 2.60 % Allowed : 11.13 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.12), residues: 5187 helix: 1.58 (0.12), residues: 1945 sheet: 0.76 (0.18), residues: 851 loop : 0.17 (0.13), residues: 2391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 247 HIS 0.006 0.001 HIS X 89 PHE 0.023 0.002 PHE C 63 TYR 0.029 0.002 TYR R 124 ARG 0.009 0.001 ARG I 40 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 823 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 702 time to evaluate : 5.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 439 HIS cc_start: 0.7190 (OUTLIER) cc_final: 0.6924 (m90) REVERT: A 583 ARG cc_start: 0.7733 (ttp-170) cc_final: 0.7385 (ttp-170) REVERT: A 841 MET cc_start: 0.9046 (mtp) cc_final: 0.8737 (mtp) REVERT: A 861 GLN cc_start: 0.8377 (tt0) cc_final: 0.8083 (mt0) REVERT: A 1310 HIS cc_start: 0.7077 (p90) cc_final: 0.6833 (p-80) REVERT: B 155 MET cc_start: 0.9204 (ttm) cc_final: 0.8977 (ttm) REVERT: B 543 GLU cc_start: 0.7882 (mt-10) cc_final: 0.7674 (mt-10) REVERT: B 840 MET cc_start: 0.3872 (mtp) cc_final: 0.3212 (pmm) REVERT: B 976 MET cc_start: 0.8859 (mtm) cc_final: 0.8644 (mtp) REVERT: B 1091 ARG cc_start: 0.8452 (ttp-110) cc_final: 0.8243 (ttp-110) REVERT: B 1125 MET cc_start: 0.8051 (mtm) cc_final: 0.7827 (mtm) REVERT: F 95 LYS cc_start: 0.7895 (OUTLIER) cc_final: 0.7653 (mmtt) REVERT: G 16 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.8087 (ptp-170) REVERT: K 22 ASN cc_start: 0.8104 (m-40) cc_final: 0.7843 (m-40) REVERT: K 23 LYS cc_start: 0.8163 (ttmt) cc_final: 0.7874 (tptt) REVERT: L 50 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.7762 (mppt) REVERT: U 51 MET cc_start: 0.2227 (mmp) cc_final: 0.1651 (mpm) REVERT: W 110 MET cc_start: 0.1248 (mmt) cc_final: 0.0849 (mmt) outliers start: 121 outliers final: 36 residues processed: 754 average time/residue: 1.6506 time to fit residues: 1520.2308 Evaluate side-chains 660 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 620 time to evaluate : 4.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1233 GLU Chi-restraints excluded: chain A residue 1244 ASN Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain A residue 1303 GLN Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 918 PHE Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 95 LYS Chi-restraints excluded: chain G residue 16 ARG Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain L residue 50 LYS Chi-restraints excluded: chain M residue 207 ASP Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 223 GLN Chi-restraints excluded: chain U residue 10 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 524 random chunks: chunk 264 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 396 optimal weight: 5.9990 chunk 324 optimal weight: 0.0980 chunk 131 optimal weight: 0.9990 chunk 476 optimal weight: 30.0000 chunk 514 optimal weight: 9.9990 chunk 424 optimal weight: 4.9990 chunk 472 optimal weight: 50.0000 chunk 162 optimal weight: 3.9990 chunk 382 optimal weight: 0.9980 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 ASN A 723 ASN A1077 ASN ** A1194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 ASN G 28 GLN M 221 ASN ** O 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 257 ASN ** O 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 223 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 45129 Z= 0.360 Angle : 0.592 11.820 61352 Z= 0.302 Chirality : 0.044 0.202 6844 Planarity : 0.004 0.054 7605 Dihedral : 13.071 155.132 6810 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.74 % Favored : 97.24 % Rotamer: Outliers : 3.34 % Allowed : 13.54 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.12), residues: 5187 helix: 1.27 (0.12), residues: 1960 sheet: 0.69 (0.18), residues: 822 loop : -0.02 (0.13), residues: 2405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 247 HIS 0.008 0.001 HIS A1445 PHE 0.031 0.002 PHE C 63 TYR 0.021 0.002 TYR A1196 ARG 0.010 0.001 ARG J 47 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 793 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 638 time to evaluate : 5.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 439 HIS cc_start: 0.7211 (OUTLIER) cc_final: 0.6970 (m90) REVERT: A 841 MET cc_start: 0.9040 (mtp) cc_final: 0.8715 (mtp) REVERT: A 1310 HIS cc_start: 0.7130 (p90) cc_final: 0.6861 (p-80) REVERT: A 1428 MET cc_start: 0.6179 (tpt) cc_final: 0.5942 (tpp) REVERT: B 299 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7218 (mp0) REVERT: B 358 GLU cc_start: 0.6819 (OUTLIER) cc_final: 0.5949 (pp20) REVERT: B 543 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7742 (mt-10) REVERT: B 554 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7354 (mp0) REVERT: B 629 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7122 (mp0) REVERT: B 840 MET cc_start: 0.3868 (mtp) cc_final: 0.3260 (pmm) REVERT: B 976 MET cc_start: 0.9035 (mtm) cc_final: 0.8720 (mtp) REVERT: B 1072 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.8035 (mmm-85) REVERT: G 16 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.8010 (ptp-170) REVERT: H 100 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7110 (mt-10) REVERT: I 82 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.6627 (mm-30) REVERT: J 31 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7144 (mt-10) REVERT: K 22 ASN cc_start: 0.8096 (m-40) cc_final: 0.7831 (m-40) REVERT: K 23 LYS cc_start: 0.8172 (ttmt) cc_final: 0.7902 (tptt) REVERT: K 68 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7437 (mm-30) REVERT: U 51 MET cc_start: 0.2398 (mmp) cc_final: 0.1841 (mpm) REVERT: X 85 MET cc_start: 0.1813 (ppp) cc_final: 0.1446 (pp-130) outliers start: 155 outliers final: 55 residues processed: 721 average time/residue: 1.5900 time to fit residues: 1408.8519 Evaluate side-chains 663 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 597 time to evaluate : 5.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 358 ARG Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1244 ASN Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 918 PHE Chi-restraints excluded: chain B residue 1072 ARG Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain G residue 16 ARG Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain H residue 103 GLU Chi-restraints excluded: chain H residue 133 HIS Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 82 GLU Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 31 GLU Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain M residue 207 ASP Chi-restraints excluded: chain M residue 299 LEU Chi-restraints excluded: chain O residue 170 SER Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain U residue 10 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 524 random chunks: chunk 470 optimal weight: 50.0000 chunk 358 optimal weight: 0.8980 chunk 247 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 227 optimal weight: 2.9990 chunk 320 optimal weight: 0.6980 chunk 478 optimal weight: 50.0000 chunk 506 optimal weight: 0.4980 chunk 249 optimal weight: 0.9980 chunk 453 optimal weight: 9.9990 chunk 136 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 ASN A 671 ASN A 723 ASN ** A1194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1230 GLN ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 GLN B 141 GLN ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1115 GLN B1120 ASN ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 ASN E 189 GLN G 28 GLN ** M 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 45129 Z= 0.242 Angle : 0.545 12.156 61352 Z= 0.278 Chirality : 0.042 0.238 6844 Planarity : 0.004 0.053 7605 Dihedral : 13.078 154.834 6810 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.89 % Favored : 97.09 % Rotamer: Outliers : 2.69 % Allowed : 15.73 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.12), residues: 5187 helix: 1.32 (0.12), residues: 1939 sheet: 0.64 (0.18), residues: 822 loop : -0.05 (0.13), residues: 2426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 247 HIS 0.005 0.001 HIS X 89 PHE 0.020 0.001 PHE A 397 TYR 0.030 0.002 TYR V 65 ARG 0.008 0.000 ARG B 608 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 755 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 630 time to evaluate : 4.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 439 HIS cc_start: 0.7165 (OUTLIER) cc_final: 0.6896 (m90) REVERT: A 447 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7701 (mt-10) REVERT: A 841 MET cc_start: 0.9034 (mtp) cc_final: 0.8684 (mtp) REVERT: A 1310 HIS cc_start: 0.7041 (p90) cc_final: 0.6755 (p-80) REVERT: B 155 MET cc_start: 0.9198 (ttm) cc_final: 0.8998 (ttm) REVERT: B 299 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.7163 (mp0) REVERT: B 629 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7081 (mp0) REVERT: B 840 MET cc_start: 0.3999 (mtp) cc_final: 0.3282 (pmm) REVERT: B 976 MET cc_start: 0.8987 (mtm) cc_final: 0.8678 (mtp) REVERT: G 16 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7989 (ptp-170) REVERT: I 82 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.6644 (mm-30) REVERT: K 22 ASN cc_start: 0.8082 (m-40) cc_final: 0.7825 (m-40) REVERT: K 23 LYS cc_start: 0.8156 (ttmt) cc_final: 0.7889 (tptt) REVERT: L 50 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.7910 (mppt) REVERT: M 107 MET cc_start: 0.6498 (ttm) cc_final: 0.5858 (mmt) REVERT: U 51 MET cc_start: 0.2338 (mmp) cc_final: 0.1779 (mpm) outliers start: 125 outliers final: 50 residues processed: 696 average time/residue: 1.6356 time to fit residues: 1404.0650 Evaluate side-chains 655 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 599 time to evaluate : 5.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1233 GLU Chi-restraints excluded: chain A residue 1244 ASN Chi-restraints excluded: chain A residue 1344 MET Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 918 PHE Chi-restraints excluded: chain B residue 1075 MET Chi-restraints excluded: chain B residue 1158 LEU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain G residue 3 TYR Chi-restraints excluded: chain G residue 16 ARG Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 103 GLU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 82 GLU Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain L residue 50 LYS Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain M residue 207 ASP Chi-restraints excluded: chain M residue 299 LEU Chi-restraints excluded: chain R residue 22 LYS Chi-restraints excluded: chain U residue 10 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 524 random chunks: chunk 421 optimal weight: 20.0000 chunk 287 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 377 optimal weight: 0.9980 chunk 208 optimal weight: 2.9990 chunk 432 optimal weight: 6.9990 chunk 350 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 258 optimal weight: 0.5980 chunk 454 optimal weight: 2.9990 chunk 127 optimal weight: 5.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 410 ASN A 723 ASN ** A1194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 654 GLN B1049 GLN B1115 GLN ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 ASN E 148 HIS G 24 ASN G 28 GLN ** M 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 109 HIS X 188 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 45129 Z= 0.414 Angle : 0.604 13.372 61352 Z= 0.307 Chirality : 0.045 0.216 6844 Planarity : 0.005 0.100 7605 Dihedral : 13.211 155.018 6810 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.99 % Favored : 96.99 % Rotamer: Outliers : 3.42 % Allowed : 15.99 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.11), residues: 5187 helix: 1.12 (0.12), residues: 1941 sheet: 0.57 (0.18), residues: 832 loop : -0.16 (0.12), residues: 2414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 453 HIS 0.006 0.001 HIS B 387 PHE 0.020 0.002 PHE M 195 TYR 0.020 0.002 TYR E 125 ARG 0.021 0.001 ARG A1286 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 768 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 609 time to evaluate : 5.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 PHE cc_start: 0.6987 (OUTLIER) cc_final: 0.6506 (m-80) REVERT: A 439 HIS cc_start: 0.7137 (OUTLIER) cc_final: 0.6893 (m90) REVERT: A 447 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7749 (mt-10) REVERT: A 535 MET cc_start: 0.8660 (ptp) cc_final: 0.8452 (ptp) REVERT: A 841 MET cc_start: 0.9059 (mtp) cc_final: 0.8731 (mtp) REVERT: B 358 GLU cc_start: 0.6836 (OUTLIER) cc_final: 0.5946 (pp20) REVERT: B 629 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.7032 (mp0) REVERT: B 796 MET cc_start: 0.8346 (OUTLIER) cc_final: 0.8141 (ttt) REVERT: B 840 MET cc_start: 0.3942 (mtp) cc_final: 0.3287 (pmm) REVERT: B 976 MET cc_start: 0.9043 (mtm) cc_final: 0.8728 (mtp) REVERT: B 1146 ILE cc_start: 0.7859 (OUTLIER) cc_final: 0.7592 (tp) REVERT: C 205 LYS cc_start: 0.9038 (OUTLIER) cc_final: 0.8375 (mmtm) REVERT: E 137 ILE cc_start: 0.7543 (OUTLIER) cc_final: 0.7114 (pp) REVERT: G 16 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.7998 (ptp-170) REVERT: H 21 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8453 (mttp) REVERT: H 100 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7176 (mt-10) REVERT: I 82 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.6648 (mm-30) REVERT: J 31 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.7127 (mt-10) REVERT: K 22 ASN cc_start: 0.8096 (m-40) cc_final: 0.7816 (m-40) REVERT: K 23 LYS cc_start: 0.8192 (ttmt) cc_final: 0.7895 (tptt) REVERT: K 68 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7507 (mm-30) REVERT: L 50 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.8063 (mmtp) REVERT: M 107 MET cc_start: 0.6454 (ttm) cc_final: 0.5803 (mmt) REVERT: U 51 MET cc_start: 0.2060 (mmp) cc_final: 0.1656 (mpm) REVERT: X 85 MET cc_start: 0.2021 (ppp) cc_final: 0.1699 (pp-130) outliers start: 159 outliers final: 66 residues processed: 698 average time/residue: 1.6207 time to fit residues: 1389.6325 Evaluate side-chains 671 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 590 time to evaluate : 5.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 PHE Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1233 GLU Chi-restraints excluded: chain A residue 1244 ASN Chi-restraints excluded: chain A residue 1344 MET Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 385 ARG Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 555 GLU Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 867 ILE Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 918 PHE Chi-restraints excluded: chain B residue 1075 MET Chi-restraints excluded: chain B residue 1146 ILE Chi-restraints excluded: chain C residue 205 LYS Chi-restraints excluded: chain C residue 253 LYS Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain G residue 3 TYR Chi-restraints excluded: chain G residue 16 ARG Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 21 LYS Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain H residue 103 GLU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 82 GLU Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 31 GLU Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain L residue 50 LYS Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain M residue 207 ASP Chi-restraints excluded: chain M residue 277 ILE Chi-restraints excluded: chain M residue 299 LEU Chi-restraints excluded: chain O residue 170 SER Chi-restraints excluded: chain Q residue 149 LEU Chi-restraints excluded: chain R residue 22 LYS Chi-restraints excluded: chain U residue 10 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 524 random chunks: chunk 170 optimal weight: 0.9990 chunk 456 optimal weight: 5.9990 chunk 100 optimal weight: 0.6980 chunk 297 optimal weight: 10.0000 chunk 125 optimal weight: 4.9990 chunk 506 optimal weight: 30.0000 chunk 420 optimal weight: 7.9990 chunk 234 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 167 optimal weight: 1.9990 chunk 266 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 ASN A 723 ASN ** A1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 HIS ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1115 GLN ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 ASN ** M 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 327 ASN ** W 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 45129 Z= 0.269 Angle : 0.568 20.411 61352 Z= 0.288 Chirality : 0.042 0.222 6844 Planarity : 0.004 0.053 7605 Dihedral : 13.194 154.777 6810 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.97 % Favored : 97.01 % Rotamer: Outliers : 2.82 % Allowed : 17.69 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.11), residues: 5187 helix: 1.17 (0.12), residues: 1950 sheet: 0.62 (0.18), residues: 811 loop : -0.15 (0.12), residues: 2426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 247 HIS 0.005 0.001 HIS W 89 PHE 0.024 0.002 PHE G 77 TYR 0.024 0.002 TYR A1196 ARG 0.009 0.000 ARG B 608 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 742 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 611 time to evaluate : 5.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.7512 (mtp85) REVERT: A 439 HIS cc_start: 0.7257 (OUTLIER) cc_final: 0.6977 (m90) REVERT: A 447 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7708 (mt-10) REVERT: A 841 MET cc_start: 0.9048 (mtp) cc_final: 0.8694 (mtp) REVERT: B 358 GLU cc_start: 0.6861 (OUTLIER) cc_final: 0.5942 (pp20) REVERT: B 629 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.7002 (mp0) REVERT: B 840 MET cc_start: 0.3954 (mtp) cc_final: 0.3206 (pmm) REVERT: B 976 MET cc_start: 0.9008 (mtm) cc_final: 0.8680 (mtp) REVERT: C 82 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8863 (mp) REVERT: C 205 LYS cc_start: 0.8998 (OUTLIER) cc_final: 0.8326 (mmtm) REVERT: E 210 GLN cc_start: 0.7067 (pp30) cc_final: 0.6748 (pp30) REVERT: G 16 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.8000 (ptp-170) REVERT: G 104 MET cc_start: 0.4762 (mtp) cc_final: 0.4466 (mpt) REVERT: H 100 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7116 (mt-10) REVERT: J 31 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.7132 (mt-10) REVERT: K 22 ASN cc_start: 0.8073 (m-40) cc_final: 0.7804 (m-40) REVERT: K 23 LYS cc_start: 0.8179 (ttmt) cc_final: 0.7886 (tptt) REVERT: L 50 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.8081 (mmtp) REVERT: M 107 MET cc_start: 0.6453 (ttm) cc_final: 0.5853 (mmt) REVERT: O 191 GLU cc_start: 0.2472 (mp0) cc_final: 0.1551 (mp0) REVERT: U 51 MET cc_start: 0.2161 (mmp) cc_final: 0.1729 (mpm) REVERT: X 85 MET cc_start: 0.2055 (ppp) cc_final: 0.1834 (pp-130) outliers start: 131 outliers final: 65 residues processed: 684 average time/residue: 1.5941 time to fit residues: 1342.8125 Evaluate side-chains 659 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 584 time to evaluate : 5.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1233 GLU Chi-restraints excluded: chain A residue 1244 ASN Chi-restraints excluded: chain A residue 1303 GLN Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 867 ILE Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 918 PHE Chi-restraints excluded: chain B residue 1075 MET Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 205 LYS Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 153 LYS Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain G residue 3 TYR Chi-restraints excluded: chain G residue 16 ARG Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain H residue 103 GLU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 31 GLU Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain L residue 50 LYS Chi-restraints excluded: chain L residue 51 ARG Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain M residue 207 ASP Chi-restraints excluded: chain M residue 245 VAL Chi-restraints excluded: chain M residue 277 ILE Chi-restraints excluded: chain M residue 299 LEU Chi-restraints excluded: chain Q residue 126 ILE Chi-restraints excluded: chain R residue 22 LYS Chi-restraints excluded: chain U residue 10 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 524 random chunks: chunk 488 optimal weight: 40.0000 chunk 57 optimal weight: 1.9990 chunk 288 optimal weight: 5.9990 chunk 370 optimal weight: 0.7980 chunk 286 optimal weight: 20.0000 chunk 426 optimal weight: 7.9990 chunk 283 optimal weight: 0.7980 chunk 505 optimal weight: 8.9990 chunk 316 optimal weight: 0.6980 chunk 307 optimal weight: 1.9990 chunk 233 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 ASN A 723 ASN ** A1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1115 GLN ** B1120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 ASN M 263 GLN ** O 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 327 ASN ** W 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 45129 Z= 0.328 Angle : 0.585 17.432 61352 Z= 0.297 Chirality : 0.043 0.224 6844 Planarity : 0.004 0.055 7605 Dihedral : 13.207 154.747 6810 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.10 % Favored : 96.88 % Rotamer: Outliers : 2.82 % Allowed : 18.25 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.11), residues: 5187 helix: 1.09 (0.12), residues: 1946 sheet: 0.59 (0.18), residues: 823 loop : -0.17 (0.12), residues: 2418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP A 247 HIS 0.026 0.001 HIS B 144 PHE 0.035 0.002 PHE R 96 TYR 0.023 0.002 TYR E 125 ARG 0.009 0.001 ARG B 608 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 730 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 599 time to evaluate : 5.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 439 HIS cc_start: 0.7241 (OUTLIER) cc_final: 0.6969 (m90) REVERT: A 447 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7687 (mt-10) REVERT: A 841 MET cc_start: 0.9055 (mtp) cc_final: 0.8708 (mtp) REVERT: A 1071 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.7670 (tm-30) REVERT: A 1428 MET cc_start: 0.6158 (tpt) cc_final: 0.5547 (mmm) REVERT: B 358 GLU cc_start: 0.6896 (OUTLIER) cc_final: 0.6005 (pp20) REVERT: B 629 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.7056 (mp0) REVERT: B 840 MET cc_start: 0.3946 (mtp) cc_final: 0.3346 (pmm) REVERT: B 976 MET cc_start: 0.9038 (mtm) cc_final: 0.8704 (mtp) REVERT: C 205 LYS cc_start: 0.9007 (OUTLIER) cc_final: 0.8344 (mmtm) REVERT: E 137 ILE cc_start: 0.7548 (OUTLIER) cc_final: 0.7100 (pp) REVERT: E 210 GLN cc_start: 0.7053 (pp30) cc_final: 0.6804 (pp30) REVERT: G 16 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.8002 (ptp-170) REVERT: G 104 MET cc_start: 0.4825 (mtp) cc_final: 0.4588 (mpt) REVERT: H 100 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7148 (mt-10) REVERT: J 31 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7130 (mt-10) REVERT: K 22 ASN cc_start: 0.8082 (m-40) cc_final: 0.7800 (m-40) REVERT: K 23 LYS cc_start: 0.8193 (ttmt) cc_final: 0.7877 (tptt) REVERT: L 50 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.8089 (mmtp) REVERT: M 107 MET cc_start: 0.6455 (ttm) cc_final: 0.5816 (mmt) REVERT: R 128 LYS cc_start: 0.5479 (OUTLIER) cc_final: 0.5116 (mttp) REVERT: U 51 MET cc_start: 0.2041 (mmp) cc_final: 0.1648 (mpm) REVERT: X 85 MET cc_start: 0.2090 (ppp) cc_final: 0.1865 (pp-130) outliers start: 131 outliers final: 74 residues processed: 674 average time/residue: 1.6172 time to fit residues: 1340.9564 Evaluate side-chains 667 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 582 time to evaluate : 5.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 358 ARG Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 902 GLU Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1071 GLU Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1233 GLU Chi-restraints excluded: chain A residue 1244 ASN Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 385 ARG Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 867 ILE Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 918 PHE Chi-restraints excluded: chain B residue 1075 MET Chi-restraints excluded: chain B residue 1158 LEU Chi-restraints excluded: chain C residue 205 LYS Chi-restraints excluded: chain C residue 253 LYS Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 95 LYS Chi-restraints excluded: chain G residue 3 TYR Chi-restraints excluded: chain G residue 16 ARG Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain H residue 103 GLU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 31 GLU Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain L residue 50 LYS Chi-restraints excluded: chain L residue 51 ARG Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 207 ASP Chi-restraints excluded: chain M residue 245 VAL Chi-restraints excluded: chain M residue 277 ILE Chi-restraints excluded: chain M residue 299 LEU Chi-restraints excluded: chain O residue 282 SER Chi-restraints excluded: chain Q residue 126 ILE Chi-restraints excluded: chain Q residue 149 LEU Chi-restraints excluded: chain R residue 22 LYS Chi-restraints excluded: chain R residue 128 LYS Chi-restraints excluded: chain R residue 166 GLU Chi-restraints excluded: chain U residue 10 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 524 random chunks: chunk 312 optimal weight: 0.9990 chunk 201 optimal weight: 0.5980 chunk 301 optimal weight: 7.9990 chunk 152 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 97 optimal weight: 0.5980 chunk 321 optimal weight: 0.8980 chunk 344 optimal weight: 2.9990 chunk 249 optimal weight: 3.9990 chunk 47 optimal weight: 0.1980 chunk 396 optimal weight: 0.2980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 ASN A 723 ASN ** A1194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 HIS ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 683 GLN ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1115 GLN ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 ASN E 71 GLN ** O 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 327 ASN R 152 ASN R 182 HIS ** W 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 45129 Z= 0.195 Angle : 0.562 19.040 61352 Z= 0.285 Chirality : 0.042 0.264 6844 Planarity : 0.004 0.055 7605 Dihedral : 13.136 154.321 6810 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.76 % Favored : 97.22 % Rotamer: Outliers : 2.37 % Allowed : 19.35 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.12), residues: 5187 helix: 1.26 (0.12), residues: 1934 sheet: 0.62 (0.18), residues: 822 loop : -0.13 (0.12), residues: 2431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP A 247 HIS 0.006 0.001 HIS D 38 PHE 0.033 0.001 PHE R 96 TYR 0.026 0.001 TYR A1196 ARG 0.008 0.000 ARG B 608 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 612 time to evaluate : 5.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 439 HIS cc_start: 0.7233 (OUTLIER) cc_final: 0.6961 (m90) REVERT: A 447 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7680 (mt-10) REVERT: A 841 MET cc_start: 0.9037 (mtp) cc_final: 0.8655 (mtp) REVERT: A 1071 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.7689 (tm-30) REVERT: A 1130 ILE cc_start: 0.7105 (tp) cc_final: 0.6778 (mm) REVERT: A 1428 MET cc_start: 0.5916 (tpt) cc_final: 0.5335 (mmm) REVERT: B 358 GLU cc_start: 0.6848 (OUTLIER) cc_final: 0.5957 (pp20) REVERT: B 629 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.7039 (mp0) REVERT: B 840 MET cc_start: 0.3769 (mtp) cc_final: 0.3133 (pmm) REVERT: B 976 MET cc_start: 0.8952 (mtm) cc_final: 0.8670 (mtp) REVERT: C 78 ILE cc_start: 0.8767 (tp) cc_final: 0.8357 (tp) REVERT: C 205 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8282 (mmtm) REVERT: G 16 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.7972 (ptp-170) REVERT: H 123 MET cc_start: 0.8975 (ttp) cc_final: 0.8751 (ttp) REVERT: I 92 LYS cc_start: 0.7528 (mmmt) cc_final: 0.7270 (tttm) REVERT: K 22 ASN cc_start: 0.8019 (m-40) cc_final: 0.7787 (m-40) REVERT: K 23 LYS cc_start: 0.8172 (ttmt) cc_final: 0.7892 (tptt) REVERT: L 50 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.8053 (mmtp) REVERT: M 107 MET cc_start: 0.6369 (ttm) cc_final: 0.5802 (mmt) REVERT: R 125 MET cc_start: 0.4927 (mtt) cc_final: 0.4521 (mmp) REVERT: U 51 MET cc_start: 0.2147 (mmp) cc_final: 0.1705 (mpm) REVERT: X 85 MET cc_start: 0.2107 (ppp) cc_final: 0.1835 (pp-130) outliers start: 110 outliers final: 52 residues processed: 673 average time/residue: 1.5461 time to fit residues: 1297.9969 Evaluate side-chains 649 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 590 time to evaluate : 4.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1071 GLU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1233 GLU Chi-restraints excluded: chain A residue 1244 ASN Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 867 ILE Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 918 PHE Chi-restraints excluded: chain B residue 1075 MET Chi-restraints excluded: chain B residue 1158 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 205 LYS Chi-restraints excluded: chain C residue 253 LYS Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 125 TYR Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain G residue 3 TYR Chi-restraints excluded: chain G residue 16 ARG Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 103 GLU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain L residue 50 LYS Chi-restraints excluded: chain L residue 51 ARG Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 245 VAL Chi-restraints excluded: chain M residue 277 ILE Chi-restraints excluded: chain M residue 299 LEU Chi-restraints excluded: chain Q residue 149 LEU Chi-restraints excluded: chain R residue 166 GLU Chi-restraints excluded: chain U residue 10 VAL Chi-restraints excluded: chain W residue 76 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 524 random chunks: chunk 459 optimal weight: 30.0000 chunk 483 optimal weight: 20.0000 chunk 441 optimal weight: 6.9990 chunk 470 optimal weight: 40.0000 chunk 283 optimal weight: 8.9990 chunk 205 optimal weight: 0.9990 chunk 369 optimal weight: 4.9990 chunk 144 optimal weight: 0.3980 chunk 425 optimal weight: 0.7980 chunk 445 optimal weight: 30.0000 chunk 469 optimal weight: 1.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 ASN A 723 ASN ** A1194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 HIS ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 683 GLN B1030 ASN ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1115 GLN ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 ASN M 263 GLN ** O 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 327 ASN ** W 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 143 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 45129 Z= 0.442 Angle : 0.659 21.664 61352 Z= 0.331 Chirality : 0.046 0.219 6844 Planarity : 0.005 0.061 7605 Dihedral : 13.238 154.429 6810 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.43 % Favored : 96.55 % Rotamer: Outliers : 2.52 % Allowed : 19.35 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.11), residues: 5187 helix: 0.99 (0.12), residues: 1947 sheet: 0.58 (0.18), residues: 821 loop : -0.18 (0.12), residues: 2419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP A 247 HIS 0.008 0.001 HIS G 4 PHE 0.029 0.002 PHE G 77 TYR 0.026 0.002 TYR E 125 ARG 0.008 0.001 ARG B 608 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 702 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 585 time to evaluate : 5.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 439 HIS cc_start: 0.7241 (OUTLIER) cc_final: 0.6940 (m90) REVERT: A 447 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7739 (mt-10) REVERT: A 700 GLN cc_start: 0.7312 (OUTLIER) cc_final: 0.6833 (tm130) REVERT: A 841 MET cc_start: 0.9066 (mtp) cc_final: 0.8726 (mtp) REVERT: A 1071 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.7906 (tm-30) REVERT: A 1130 ILE cc_start: 0.7164 (tp) cc_final: 0.6821 (mm) REVERT: A 1428 MET cc_start: 0.6201 (tpt) cc_final: 0.5566 (mmm) REVERT: B 358 GLU cc_start: 0.6935 (OUTLIER) cc_final: 0.6059 (pp20) REVERT: B 629 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.7058 (mp0) REVERT: B 796 MET cc_start: 0.8355 (OUTLIER) cc_final: 0.8151 (ttt) REVERT: B 840 MET cc_start: 0.4018 (mtp) cc_final: 0.3311 (pmm) REVERT: B 976 MET cc_start: 0.9063 (mtm) cc_final: 0.8721 (mtp) REVERT: C 205 LYS cc_start: 0.9022 (OUTLIER) cc_final: 0.8340 (mmtm) REVERT: E 110 MET cc_start: 0.6465 (tpp) cc_final: 0.6178 (tpp) REVERT: G 16 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.7999 (ptp-170) REVERT: J 41 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.8215 (mmtm) REVERT: K 22 ASN cc_start: 0.8062 (m-40) cc_final: 0.7798 (m-40) REVERT: K 23 LYS cc_start: 0.8218 (ttmt) cc_final: 0.7890 (tptt) REVERT: M 107 MET cc_start: 0.6402 (ttm) cc_final: 0.5818 (mmt) REVERT: R 125 MET cc_start: 0.4900 (mtt) cc_final: 0.4459 (mmp) REVERT: U 51 MET cc_start: 0.2293 (mmp) cc_final: 0.1795 (mpm) REVERT: X 85 MET cc_start: 0.2104 (ppp) cc_final: 0.1848 (pp-130) outliers start: 117 outliers final: 65 residues processed: 655 average time/residue: 1.5530 time to fit residues: 1268.4802 Evaluate side-chains 640 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 566 time to evaluate : 5.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 700 GLN Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1071 GLU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1233 GLU Chi-restraints excluded: chain A residue 1244 ASN Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 385 ARG Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 738 THR Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 867 ILE Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 918 PHE Chi-restraints excluded: chain B residue 1075 MET Chi-restraints excluded: chain B residue 1158 LEU Chi-restraints excluded: chain C residue 205 LYS Chi-restraints excluded: chain C residue 253 LYS Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 95 LYS Chi-restraints excluded: chain G residue 3 TYR Chi-restraints excluded: chain G residue 16 ARG Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 103 GLU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 41 LYS Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 99 SER Chi-restraints excluded: chain M residue 31 ASP Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 245 VAL Chi-restraints excluded: chain M residue 277 ILE Chi-restraints excluded: chain M residue 299 LEU Chi-restraints excluded: chain O residue 282 SER Chi-restraints excluded: chain Q residue 149 LEU Chi-restraints excluded: chain R residue 166 GLU Chi-restraints excluded: chain U residue 10 VAL Chi-restraints excluded: chain W residue 76 MET Chi-restraints excluded: chain W residue 168 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 524 random chunks: chunk 309 optimal weight: 0.8980 chunk 497 optimal weight: 30.0000 chunk 303 optimal weight: 2.9990 chunk 236 optimal weight: 0.5980 chunk 345 optimal weight: 0.7980 chunk 522 optimal weight: 30.0000 chunk 480 optimal weight: 50.0000 chunk 415 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 321 optimal weight: 0.1980 chunk 254 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 ASN A 723 ASN ** A1194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 GLN B 144 HIS ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1030 ASN ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1115 GLN ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 ASN D 43 HIS ** O 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 327 ASN ** W 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 45129 Z= 0.233 Angle : 0.612 23.642 61352 Z= 0.307 Chirality : 0.043 0.237 6844 Planarity : 0.004 0.068 7605 Dihedral : 13.190 154.011 6810 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.97 % Favored : 97.01 % Rotamer: Outliers : 1.64 % Allowed : 20.49 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.12), residues: 5187 helix: 1.10 (0.12), residues: 1940 sheet: 0.56 (0.18), residues: 818 loop : -0.16 (0.13), residues: 2429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.002 TRP A 247 HIS 0.006 0.001 HIS B 144 PHE 0.026 0.002 PHE M 195 TYR 0.027 0.002 TYR A1196 ARG 0.011 0.000 ARG I 40 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10374 Ramachandran restraints generated. 5187 Oldfield, 0 Emsley, 5187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 582 time to evaluate : 5.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 439 HIS cc_start: 0.7217 (OUTLIER) cc_final: 0.6916 (m90) REVERT: A 447 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7679 (mt-10) REVERT: A 700 GLN cc_start: 0.7281 (OUTLIER) cc_final: 0.6820 (tm130) REVERT: A 841 MET cc_start: 0.9041 (mtp) cc_final: 0.8666 (mtp) REVERT: A 1071 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.7716 (tm-30) REVERT: A 1130 ILE cc_start: 0.7112 (tp) cc_final: 0.6783 (mm) REVERT: A 1428 MET cc_start: 0.5820 (tpt) cc_final: 0.5381 (mmm) REVERT: B 358 GLU cc_start: 0.6935 (OUTLIER) cc_final: 0.6028 (pp20) REVERT: B 629 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7060 (mp0) REVERT: B 840 MET cc_start: 0.3775 (mtp) cc_final: 0.3055 (pmm) REVERT: B 976 MET cc_start: 0.8998 (mtm) cc_final: 0.8707 (mtp) REVERT: C 205 LYS cc_start: 0.8942 (OUTLIER) cc_final: 0.8281 (mmtm) REVERT: G 16 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.7940 (ptp-170) REVERT: K 22 ASN cc_start: 0.8019 (m-40) cc_final: 0.7780 (m-40) REVERT: K 23 LYS cc_start: 0.8172 (ttmt) cc_final: 0.7876 (tptt) REVERT: M 107 MET cc_start: 0.6440 (ttm) cc_final: 0.5891 (mmt) REVERT: R 125 MET cc_start: 0.4850 (mtt) cc_final: 0.4454 (mmp) REVERT: U 51 MET cc_start: 0.2209 (mmp) cc_final: 0.1714 (mpm) REVERT: X 85 MET cc_start: 0.2148 (ppp) cc_final: 0.1914 (pp-130) outliers start: 76 outliers final: 54 residues processed: 624 average time/residue: 1.6067 time to fit residues: 1239.1853 Evaluate side-chains 632 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 571 time to evaluate : 5.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain A residue 700 GLN Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 1071 GLU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1244 ASN Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 738 THR Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 867 ILE Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 1075 MET Chi-restraints excluded: chain B residue 1158 LEU Chi-restraints excluded: chain C residue 205 LYS Chi-restraints excluded: chain C residue 253 LYS Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 95 LYS Chi-restraints excluded: chain G residue 3 TYR Chi-restraints excluded: chain G residue 16 ARG Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 103 GLU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain M residue 31 ASP Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 245 VAL Chi-restraints excluded: chain M residue 277 ILE Chi-restraints excluded: chain M residue 299 LEU Chi-restraints excluded: chain O residue 282 SER Chi-restraints excluded: chain Q residue 149 LEU Chi-restraints excluded: chain R residue 166 GLU Chi-restraints excluded: chain U residue 10 VAL Chi-restraints excluded: chain W residue 76 MET Chi-restraints excluded: chain W residue 168 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 524 random chunks: chunk 330 optimal weight: 40.0000 chunk 442 optimal weight: 30.0000 chunk 127 optimal weight: 5.9990 chunk 383 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 115 optimal weight: 8.9990 chunk 416 optimal weight: 8.9990 chunk 174 optimal weight: 0.0570 chunk 427 optimal weight: 5.9990 chunk 52 optimal weight: 0.0980 chunk 76 optimal weight: 0.7980 overall best weight: 0.7700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 ASN A 410 ASN A 723 ASN ** A1194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 GLN B 144 HIS ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1115 GLN ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 ASN M 263 GLN ** O 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.211443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.152758 restraints weight = 55343.014| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 2.27 r_work: 0.3382 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 45129 Z= 0.246 Angle : 0.613 23.706 61352 Z= 0.308 Chirality : 0.043 0.295 6844 Planarity : 0.004 0.064 7605 Dihedral : 13.169 153.879 6810 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.12 % Favored : 96.86 % Rotamer: Outliers : 1.89 % Allowed : 20.36 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.43 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.12), residues: 5187 helix: 1.16 (0.12), residues: 1928 sheet: 0.55 (0.18), residues: 825 loop : -0.20 (0.12), residues: 2434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.002 TRP A 247 HIS 0.011 0.001 HIS B 144 PHE 0.033 0.002 PHE M 304 TYR 0.022 0.001 TYR E 8 ARG 0.010 0.000 ARG B 608 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19464.37 seconds wall clock time: 346 minutes 57.34 seconds (20817.34 seconds total)